Abstract:The Speckled Dace, Rhinichthys osculus (Girard), is a small species of fish (Cypriniformes, Leuciscidae) that has the widest geographic range of any freshwater dispersing fish in western North America. The dynamic geologic history of the region has produced many isolated watersheds with endemic fish species. However, Speckled Dace from these watersheds cannot be differentiated readily by morphometrics and meristics. This has led to the widely accepted hypothesis that the dace’s adaptability and ability to cros… Show more
“…Finally, the use of an appropriate repository—in our case the Oregon State University Ichthyology Collection—that links DNA extracts, tissues, specimens and genomic data permits the re‐evaluation of specimen assignment when taxonomies are revised, ensuring that the collection remains valid and current. For example, a 2023 assessment of the Rhinichthys osculus species complex (Moyle et al, 2023) revised the taxonomic designations of our dace specimens during final review of our manuscript. This highlights the point that a collection of this nature is not static and needs maintenance.…”
Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error‐free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial ‘barcode’ regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
“…Finally, the use of an appropriate repository—in our case the Oregon State University Ichthyology Collection—that links DNA extracts, tissues, specimens and genomic data permits the re‐evaluation of specimen assignment when taxonomies are revised, ensuring that the collection remains valid and current. For example, a 2023 assessment of the Rhinichthys osculus species complex (Moyle et al, 2023) revised the taxonomic designations of our dace specimens during final review of our manuscript. This highlights the point that a collection of this nature is not static and needs maintenance.…”
Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error‐free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial ‘barcode’ regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
“…However, Foskett daces do differ enough in microsatellite allele frequencies to merit recognition as a distinct and significant population [ 27 ] within a subspecies of Western Speckled Dace inhabiting the entire Warner Valley. Moyle et al [ 41 ] recognized this subspecies formally as Rhinichthys klamathensis goyatoka. Fig.…”
Foskett Spring in Oregon’s desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace’s recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population’s surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate that persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada’s Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace fewer than 1000 years ago, much more recently than previously suspected and possibly coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.
“…However, Foskett daces do differ enough in microsatellite allele frequencies to merit recognition as a distinct and significant population (Hoekzema & Sidlauskas, 2014) within a subspecies of Western Speckled Daces inhabiting the entire Warner Valley. Moyle et al (2023) recognized this subspecies formally as Rhinichthys klamathensis goyatoka.…”
Foskett Spring in Oregon's desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace's recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population's surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate the phenomenon of persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5,000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada's Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace just 600 years ago, much more recently than previously suspected and coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.
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